private void SetCompareTable(IAtomContainer mol)
{
this.compare = mol;
this.compareTable = MorganNumbersTools.GetMorganNumbers(compare);
sortedCompareTable = new long[compareTable.Length];
Array.Copy(compareTable, 0, sortedCompareTable, 0, compareTable.Length);
Array.Sort(sortedCompareTable);
}
private void SetBaseTable(IAtomContainer mol)
{
this.base_ = mol;
this.baseTable = MorganNumbersTools.GetMorganNumbers(base_);
sortedBaseTable = new long[baseTable.Length];
Array.Copy(baseTable, 0, sortedBaseTable, 0, baseTable.Length);
Array.Sort(sortedBaseTable);
}
/// <summary>
/// Says if an atom as a center of any valid stereo configuration or not.
/// This method uses wedge bonds. 3D coordinates are not taken into account. If there
/// are no wedge bonds around a potential stereo center, it will not be found.
/// </summary>
/// <param name="stereoAtom">The atom which is the center</param>
/// <param name="container">The atomContainer the atom is in</param>
/// <returns>true=is a stereo atom, false=is not</returns>
public static bool IsStereo(IAtomContainer container, IAtom stereoAtom)
{
var atoms = container.GetConnectedAtoms(stereoAtom).ToReadOnlyList();
if (atoms.Count < 4 || atoms.Count > 6)
{
return(false);
}
var bonds = container.GetConnectedBonds(stereoAtom);
int stereo = 0;
foreach (var bond in bonds)
{
if (bond.Stereo != BondStereo.None)
{
stereo++;
}
}
if (stereo == 0)
{
return(false);
}
int differentAtoms = 0;
for (int i = 0; i < atoms.Count; i++)
{
bool isDifferent = true;
for (int k = 0; k < i; k++)
{
if (atoms[i].Symbol.Equals(atoms[k].Symbol, StringComparison.Ordinal))
{
isDifferent = false;
break;
}
}
if (isDifferent)
{
differentAtoms++;
}
}
if (differentAtoms != atoms.Count)
{
long[] morgannumbers = MorganNumbersTools.GetMorganNumbers(container);
var differentSymbols = new List <string>();
foreach (var atom in atoms)
{
if (!differentSymbols.Contains(atom.Symbol))
{
differentSymbols.Add(atom.Symbol);
}
}
int[] onlyRelevantIfTwo = new int[2];
if (differentSymbols.Count == 2)
{
foreach (var atom in atoms)
{
if (differentSymbols.IndexOf(atom.Symbol) == 0)
{
onlyRelevantIfTwo[0]++;
}
else
{
onlyRelevantIfTwo[1]++;
}
}
}
bool[] symbolsWithDifferentMorganNumbers = new bool[differentSymbols.Count];
var symbolsMorganNumbers = new List <long> [symbolsWithDifferentMorganNumbers.Length];
for (int i = 0; i < symbolsWithDifferentMorganNumbers.Length; i++)
{
symbolsWithDifferentMorganNumbers[i] = true;
symbolsMorganNumbers[i] = new List <long>();
}
foreach (var atom in atoms)
{
int elementNumber = differentSymbols.IndexOf(atom.Symbol);
if (symbolsMorganNumbers[elementNumber].Contains(morgannumbers[container.Atoms.IndexOf(atom)]))
{
symbolsWithDifferentMorganNumbers[elementNumber] = false;
}
else
{
symbolsMorganNumbers[elementNumber].Add(morgannumbers[container.Atoms.IndexOf(atom)]);
}
}
int numberOfSymbolsWithDifferentMorganNumbers = 0;
foreach (var symbolWithDifferentMorganNumber in symbolsWithDifferentMorganNumbers)
{
if (symbolWithDifferentMorganNumber)
{
numberOfSymbolsWithDifferentMorganNumbers++;
}
}
if (numberOfSymbolsWithDifferentMorganNumbers != differentSymbols.Count)
{
if ((atoms.Count == 5 || atoms.Count == 6) &&
(numberOfSymbolsWithDifferentMorganNumbers + differentAtoms > 2 || (differentAtoms == 2 &&
onlyRelevantIfTwo[0] > 1 && onlyRelevantIfTwo[1] > 1)))
{
return(true);
}
return(IsSquarePlanar(container, stereoAtom) &&
(numberOfSymbolsWithDifferentMorganNumbers + differentAtoms > 2 || (differentAtoms == 2 &&
onlyRelevantIfTwo[0] > 1 && onlyRelevantIfTwo[1] > 1)));
}
}
return(true);
}